Comparative Mapping Suggests Repeated Selection of the Same Quantitative Trait Locus for High Leaf Photosynthesis Rate in Rice High-Yield Breeding Programs

Rice (Oryza sativa L.) yield is determined by the relationship between sink, source, and plant architecture. 'Takanari', a high-yielding rice variety descended from 'IR8' and 'Tongil', shows a semidwarf plant stature and has a large sink size and high photosynthesis rate. Previous studies have revealed that alleles of semi-dwarf1 (sd1) and GRAIN NUMBER1A (GN1A), which confer a semidwarf plant type and large panicles, respectively, have been selected repeatedly in breeding programs during the process of breeding for high yield. Until now, however, no genetic factors related to photosynthesis have been identified as having been selected in breeding programs. In this study, we conducted comparative mapping of quantitative trait loci (QTLs) for photosynthesis-related traits using three F-2 populations: 'Koshihikari' x Takanari, Koshihikari x Tongil, and Koshihikari x IR8. Comparison of QTL locations in the three populations revealed a QTL in the same location on the long arm of chromosome 4 in each one, with the allele for higher photosynthesis-related traits coming from the higher-yielding parent of each population. Further genotypic analysis of the Takanari pedigree revealed the same genotype on the long arm of chromosome 4 in varieties related to IR8 and Takanari. These results suggest that breeders have selected the favorable allele of the QTL for photosynthesis on chromosome 4 in several breeding programs for high yield.